How do I build an A- or B-form DNA model with a particular base sequence?
The easiest way to build a canonical double helical structure of specific sequence is to use the fiber program. The default option is structure #4, which corresponds to the calf thymus B-DNA double helix due to Struther Arnott. To build the A-form, the user should choose structure #1. The program will automatically request the desired sequence of bases (A, C, G, T). Coordinates of these two structures are taken from Struther Arnott: “Polynucleotide secondary structures: an historical perspective”, pp. 1-38 in “Oxford Handbook of Nucleic Acid Structure”, edited by Stephen Neidle (Oxford Press, 1999).
